AMBER: sander, MD problems

From: Kepa Koldo Burusco Goņi <KepaKoldo.Burusco.campus.uab.es>
Date: Mon, 22 Nov 2004 13:00:37 +0100

22-XI-2004

Dear Amber users;

I am trying to run some molecular dynamics of a box of solvent (299 molecules,
100 Angstrom length, V = constant, gradually heating from 0K to 375K) in
several machines with Amber7, but the calculations blow up unexpectedly when I
try to run them on a LINUX PC server (SuSE 9.0).

It is strange because the same files work correctly (and also slowly) in an
older SGI Octane machine (much slower than the PC).

I have checked the output files and the finale lines of "file.out" show this
error message:
********************************************************

------------------------------------------------------------------------------ 
--
   4.  RESULTS
------------------------------------------------------------------------------
--
 ---------------------------------------------------
 APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
 using   5000.0 points per unit in tabled values
 TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err =   0.3242E-14   at   2.436720
| CHECK d/dx switch(x): max rel err =   0.7977E-11   at   2.712040
 ---------------------------------------------------
| Local SIZE OF NONBOND LIST =    1013859
| TOTAL SIZE OF NONBOND LIST =    1013859
 Exceeding lastrst
   lastrst =      2000000
   top_stk=      1050602
   isize  =      1060904
   request=      2111506
  Increase lastrst in the &cntrl namelist
******************************************************
.... It seems to be any kind of problem with "lastrst" option but I cannot find
it in the manual...
Do anyone have any idea? What should I do?
I also send the "file.in" and "file.out" in case you need more information.
Thank you very much in advance!!!
Kepa K. Burusco Goņi
e-mail; kepakoldo.burusco.campus.uab.es
tfno: 0034 93 581 1266
Universidad Autonoma de Barcelona
Campus de Bellaterra
BARCELONA
Spain.

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Received on Mon Nov 22 2004 - 12:53:00 PST
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